title: Envelope: interactive software for modeling and fitting complex isotope distributions.
abstract: BACKGROUND
  An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope labeling patterns. These patterns can be quite complex, in particular with in vivo metabolic labeling experiments producing fractional atomic labeling or fractional residue labeling of peptides or other macromolecules. In general, it can be difficult to distinguish the contributions of species with different labeling patterns to an experimental spectrum and difficult to calculate a theoretical isotope distribution to fit such data. There is a need for interactive and user-friendly software that can calculate and fit the entire isotope distribution of a complex mixture while comparing these calculations with experimental data and extracting the contributions from the differently labeled species.
  
  
  RESULTS
  Envelope has been developed to be user-friendly while still being as flexible and powerful as possible. Envelope can simultaneously calculate the isotope distributions for any number of different labeling patterns for a given peptide or oligonucleotide, while automatically summing these into a single overall isotope distribution. Envelope can handle fractional or complete atom or residue-based labeling, and the contribution from each different user-defined labeling pattern is clearly illustrated in the interactive display and is individually adjustable. At present, Envelope supports labeling with 2H, 13C, and 15N, and supports adjustments for baseline correction, an instrument accuracy offset in the m/z domain, and peak width. Furthermore, Envelope can display experimental data superimposed on calculated isotope distributions, and calculate a least-squares goodness of fit between the two. All of this information is displayed on the screen in a single graphical user interface. Envelope supports high-quality output of experimental and calculated distributions in PNG or PDF format. Beyond simply comparing calculated distributions to experimental data, Envelope is useful for planning or designing metabolic labeling experiments, by visualizing hypothetical isotope distributions in order to evaluate the feasibility of a labeling strategy. Envelope is also useful as a teaching tool, with its real-time display capabilities providing a straightforward way to illustrate the key variable factors that contribute to an observed isotope distribution.
  
  
  CONCLUSIONS
  Envelope is a powerful tool for the interactive calculation and visualization of complex isotope distributions for comparison to experimental data. It is available under the GNU General Public License from http://williamson.scripps.edu/envelope/.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. sykes@scripps.edu
authors.forename: Michael T
authors.initials: MT
authors.lastname: Sykes
authors.forename: James R
authors.initials: JR
authors.lastname: Williamson
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000032:analysis; D019295:Computational Biology / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D007553:Isotope Labeling / Q000379:methods; D007554:Isotopes / Q000032:analysis* / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods; D008956:Models, Chemical; D009841:Oligonucleotides / Q000032:analysis / Q000737:chemistry; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D007554:Isotopes; D009841:Oligonucleotides; D010455:Peptides